Engineering Cellular Metabolism

[1]  William C. Deloache,et al.  A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. , 2015, ACS synthetic biology.

[2]  Robert L. Campbell,et al.  ESCHERICHIA COLI K-12* , 1973 .

[3]  A. Tøndervik,et al.  Random Mutagenesis of the Pm Promoter as a Powerful Strategy for Improvement of Recombinant-Gene Expression , 2009, Applied and Environmental Microbiology.

[4]  Zhengxiang Wang,et al.  Metabolic engineering of Escherichia coli: a sustainable industrial platform for bio-based chemical production. , 2013, Biotechnology advances.

[5]  J. Keasling,et al.  Homogeneous expression of the P(BAD) promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. , 2001, Microbiology.

[6]  Ole Winther,et al.  Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae , 2006, Genome Biology.

[7]  Martin Dragosits,et al.  Adaptive laboratory evolution – principles and applications for biotechnology , 2013, Microbial Cell Factories.

[8]  Brian F. Pfleger,et al.  Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production , 2008, Applied and Environmental Microbiology.

[9]  B. Hallström,et al.  Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast , 2015, Proceedings of the National Academy of Sciences.

[10]  G. Stephanopoulos,et al.  Global transcription machinery engineering: a new approach for improving cellular phenotype. , 2007, Metabolic engineering.

[11]  John R Yates,et al.  Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator , 2009, Molecular systems biology.

[12]  Christopher A. Voigt,et al.  Automated design of synthetic ribosome binding sites to control protein expression , 2016 .

[13]  Edward J. O'Brien,et al.  Computing the functional proteome: recent progress and future prospects for genome-scale models. , 2015, Current opinion in biotechnology.

[14]  J. Nielsen,et al.  De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae. , 2015, Metabolic engineering.

[15]  J J Valdes,et al.  A comparative study of global stress gene regulation in response to overexpression of recombinant proteins in Escherichia coli. , 2000, Metabolic engineering.

[16]  J. Keasling,et al.  Engineering a mevalonate pathway in Escherichia coli for production of terpenoids , 2003, Nature Biotechnology.

[17]  J. Keasling,et al.  Engineering dynamic pathway regulation using stress-response promoters , 2013, Nature Biotechnology.

[18]  Sang Yup Lee,et al.  Recent advances in reconstruction and applications of genome-scale metabolic models. , 2012, Current opinion in biotechnology.

[19]  Jay D Keasling,et al.  Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. , 2013, ACS synthetic biology.

[20]  Timothy S. Ham,et al.  Production of the antimalarial drug precursor artemisinic acid in engineered yeast , 2006, Nature.

[21]  Jay D. Keasling,et al.  A Propionate-Inducible Expression System for Enteric Bacteria , 2005, Applied and Environmental Microbiology.

[22]  V. Siewers,et al.  Advances in yeast genome engineering. , 2014, FEMS yeast research.

[23]  Edward J. O'Brien,et al.  Using Genome-scale Models to Predict Biological Capabilities , 2015, Cell.

[24]  Patrick H. Bradley,et al.  Growth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations , 2010, Molecular biology of the cell.

[25]  Y. Choi,et al.  Microbial production of short-chain alkanes , 2013, Nature.

[26]  Jasmine L. Gallaher,et al.  Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction , 2010, Science.

[27]  C. Smolke,et al.  Complete biosynthesis of opioids in yeast , 2015, Science.

[28]  L. Wackett An annotated selection of World Wide Web sites relevant to the topics in Microbial Biotechnology , 2013, Microbial biotechnology.

[29]  Kirsten R Benjamin,et al.  Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis. , 2014, Metabolic engineering.

[30]  J. Nielsen,et al.  Uncovering transcriptional regulation of metabolism by using metabolic network topology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Jay D Keasling,et al.  Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. , 2007, Metabolic engineering.

[32]  Luke A. Gilbert,et al.  CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes , 2013, Cell.

[33]  J. Park,et al.  Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs , 2013, Nature Biotechnology.

[34]  Jens Nielsen,et al.  Profiling of Cytosolic and Peroxisomal Acetyl-CoA Metabolism in Saccharomyces cerevisiae , 2012, PloS one.

[35]  Keith E. J. Tyo,et al.  Stabilized gene duplication enables long-term selection-free heterologous pathway expression , 2009, Nature Biotechnology.

[36]  Sergio Bordel,et al.  Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors. , 2015, Integrative biology : quantitative biosciences from nano to macro.

[37]  Jay D Keasling,et al.  Programming adaptive control to evolve increased metabolite production , 2013, Nature Communications.

[38]  V. Vinci,et al.  Production of Cephalosporin Intermediates by Feeding Adipic Acid to Recombinant Penicillium chrysogenum Strains Expressing Ring Expansion Activity , 1995, Bio/Technology.

[39]  Paul D. Cotter Bioengineering , 2012, Bioengineered.

[40]  S. Lee,et al.  Metabolic engineering of Corynebacterium glutamicum for L-arginine production , 2011, Nature Communications.

[41]  Brian F. Pfleger,et al.  Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes , 2006, Nature Biotechnology.

[42]  A. Krivoruchko,et al.  Microbial acetyl-CoA metabolism and metabolic engineering. , 2015, Metabolic engineering.

[43]  J. Keasling,et al.  Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids , 2012, Nature Biotechnology.

[44]  G. Church,et al.  Large-scale de novo DNA synthesis: technologies and applications , 2014, Nature Methods.

[45]  B. Palsson,et al.  Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth , 2002, Nature.

[46]  Donghyuk Kim,et al.  Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. , 2015, Cell reports.

[47]  J. Liao,et al.  Engineering of Escherichia coli central metabolism for aromatic metabolite production with near theoretical yield , 1994, Applied and environmental microbiology.

[48]  Jens Nielsen,et al.  Metabolic engineering of -lactam production , 2003 .

[49]  Steve C. C. Shih,et al.  A Versatile Microfluidic Device for Automating Synthetic Biology. , 2015, ACS synthetic biology.

[50]  Hal S Alper,et al.  The synthetic biology toolbox for tuning gene expression in yeast. , 2014, FEMS yeast research.

[51]  Jens Nielsen,et al.  Application of genome-scale metabolic models in metabolic engineering , 2013 .

[52]  Jens Nielsen,et al.  Improving Production of Malonyl Coenzyme A-Derived Metabolites by Abolishing Snf1-Dependent Regulation of Acc1 , 2014, mBio.

[53]  AC Tose Cell , 1993, Cell.

[54]  A. Komar,et al.  Internal Ribosome Entry Sites in Cellular mRNAs: Mystery of Their Existence* , 2005, Journal of Biological Chemistry.

[55]  K. Benjamin,et al.  Engineering Acetyl Coenzyme A Supply: Functional Expression of a Bacterial Pyruvate Dehydrogenase Complex in the Cytosol of Saccharomyces cerevisiae , 2014, mBio.

[56]  K. Hammer,et al.  The Sequence of Spacers between the Consensus Sequences Modulates the Strength of Prokaryotic Promoters , 1998, Applied and Environmental Microbiology.

[57]  Jens Nielsen,et al.  The roles of galactitol, galactose‐1‐phosphate, and phosphoglucomutase in galactose‐induced toxicity in Saccharomyces cerevisiae , 2008, Biotechnology and bioengineering.

[58]  Jens Nielsen,et al.  Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode. , 2012, Metabolic engineering.

[59]  Amir Feizi,et al.  Altered sterol composition renders yeast thermotolerant , 2014, Science.

[60]  Michael J. Paulus,et al.  Bioluminescent-bioreporter integrated circuits form novel whole-cell biosensors , 1998 .

[61]  J. Nielsen,et al.  Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory , 2013, PloS one.

[62]  J. Nielsen,et al.  Establishment of a yeast platform strain for production of p-coumaric acid through metabolic engineering of aromatic amino acid biosynthesis. , 2015, Metabolic engineering.

[63]  Jay D. Keasling,et al.  Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin , 2012, Proceedings of the National Academy of Sciences.

[64]  Frances H Arnold,et al.  Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution. , 2015, Angewandte Chemie.

[65]  Edward J. O'Brien,et al.  Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli , 2014, Nature Communications.

[66]  Jens Nielsen,et al.  Economic and environmental impacts of microbial biodiesel , 2013, Nature Biotechnology.

[67]  J. Pronk,et al.  De novo production of the flavonoid naringenin in engineered Saccharomyces cerevisiae , 2012, Microbial Cell Factories.

[68]  V. Marx Targeted proteomics , 2013, Nature Methods.

[69]  Peter Saling,et al.  Eco-Efficiency Analysis of biotechnological processes , 2005, Applied Microbiology and Biotechnology.

[70]  Jens Nielsen,et al.  Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism. , 2013, Metabolic engineering.

[71]  Jens Nielsen,et al.  Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network , 2000, Nature Biotechnology.

[72]  J. Liao,et al.  Pathway engineering for production of aromatics in Escherichia coli: Confirmation of stoichiometric analysis by independent modulation of AroG, TktA, and Pps activities , 1995, Biotechnology and bioengineering.

[73]  Jens Nielsen,et al.  Synthetic Biology for Engineering Acetyl Coenzyme A Metabolism in Yeast , 2014, mBio.

[74]  Keith E. J. Tyo,et al.  Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli , 2010, Science.

[75]  Jack T Pronk,et al.  Evolutionary engineering of mixed-sugar utilization by a xylose-fermenting Saccharomyces cerevisiae strain. , 2005, FEMS yeast research.

[76]  Constantine D. Spyropoulos,et al.  Machine Learning and Its Applications , 2001, Lecture Notes in Computer Science.

[77]  B. Ensley,et al.  Construction of Metabolic Operons Catalyzing the De Novo Biosynthesis of Indigo in Escherichia coli , 1993, Bio/Technology.

[78]  H. Salis The ribosome binding site calculator. , 2011, Methods in enzymology.

[79]  Alexander Vainstein,et al.  Harnessing yeast subcellular compartments for the production of plant terpenoids. , 2011, Metabolic engineering.

[80]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[81]  R. Hampton,et al.  Effects of overproduction of the catalytic domain of 3-hydroxy-3-methylglutaryl coenzyme A reductase on squalene synthesis in Saccharomyces cerevisiae , 1997, Applied and environmental microbiology.

[82]  V. Hatzimanikatis,et al.  Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. , 2015, Current opinion in chemical biology.

[83]  J. Bailey,et al.  Toward a science of metabolic engineering , 1991, Science.

[84]  Frederick C. Neidhardt,et al.  Physiology of the bacterial cell , 1990 .

[85]  S. Lee,et al.  Systems strategies for developing industrial microbial strains , 2015, Nature Biotechnology.

[86]  Christina D. Smolke,et al.  Coordinated, Differential Expression of Two Genes through Directed mRNA Cleavage and Stabilization by Secondary Structures , 2000, Applied and Environmental Microbiology.

[87]  J. Keasling,et al.  Targeted proteomics for metabolic pathway optimization: application to terpene production. , 2011, Metabolic engineering.

[88]  J Villadsen,et al.  Optimization of ethanol production in Saccharomyces cerevisiae by metabolic engineering of the ammonium assimilation. , 2000, Metabolic engineering.

[89]  Sara Hooshangi,et al.  Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli. , 2010, Metabolic engineering.

[90]  G. Stephanopoulos,et al.  Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption , 2014, Nature Biotechnology.

[91]  Nathan J Hillson,et al.  DeviceEditor visual biological CAD canvas , 2012, Journal of Biological Engineering.

[92]  W. R. Farmer,et al.  Improving lycopene production in Escherichia coli by engineering metabolic control , 2000, Nature Biotechnology.

[93]  G. Stephanopoulos,et al.  Network rigidity and metabolic engineering in metabolite overproduction , 1991, Science.

[94]  Sorin Draghici,et al.  Machine Learning and Its Applications to Biology , 2007, PLoS Comput. Biol..

[95]  J. Nielsen,et al.  Yeast cell factories on the horizon , 2015, Science.

[96]  Pamela A. Silver,et al.  Engineering a Synthetic Dual-Organism System for Hydrogen Production , 2009, Applied and Environmental Microbiology.

[97]  S. Lee,et al.  Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation , 2007, Proceedings of the National Academy of Sciences.

[98]  アルパー,ハル,エス.,et al.  Global transcription machinery engineering , 2006 .

[99]  J. Keasling,et al.  Recent applications of synthetic biology tools for yeast metabolic engineering. , 2014, FEMS yeast research.

[100]  M. Brynildsen,et al.  Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production , 2012, Nature Biotechnology.

[101]  Jay D Keasling,et al.  Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. , 2015, Metabolic engineering.

[102]  J. Keasling,et al.  High-level semi-synthetic production of the potent antimalarial artemisinin , 2013, Nature.

[103]  Gabriel C. Wu,et al.  Synthetic protein scaffolds provide modular control over metabolic flux , 2009, Nature Biotechnology.

[104]  Jens Nielsen,et al.  Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis , 2011, Proceedings of the National Academy of Sciences.

[105]  C. Nakamura,et al.  Metabolic engineering for the microbial production of 1,3-propanediol. , 2003, Current opinion in biotechnology.

[106]  M. Gerstein,et al.  Genomic analysis of the hierarchical structure of regulatory networks , 2006, Proceedings of the National Academy of Sciences.

[107]  B. Jiang,et al.  Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine , 2015, Nature Communications.

[108]  Hal S. Alper,et al.  The development and characterization of synthetic minimal yeast promoters , 2015, Nature Communications.

[109]  Meghdad Hajimorad,et al.  BglBrick vectors and datasheets: A synthetic biology platform for gene expression , 2011, Journal of biological engineering.

[110]  A. Burgard,et al.  Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. , 2011, Nature chemical biology.

[111]  Jian Chen,et al.  Overview of Regulatory Strategies and Molecular Elements in Metabolic Engineering of Bacteria , 2012, Molecular Biotechnology.

[112]  Jens Nielsen,et al.  Systems biology of lipid metabolism: From yeast to human , 2009, FEBS letters.

[113]  J. Nielsen,et al.  It Is All about Metabolic Fluxes , 2003 .

[114]  J. Keasling Manufacturing Molecules Through Metabolic Engineering , 2010, Science.

[115]  G. Stephanopoulos,et al.  Compartmentalization of metabolic pathways in yeast mitochondria improves production of branched chain alcohols , 2013, Nature Biotechnology.

[116]  A. Krivoruchko,et al.  Functional pyruvate formate lyase pathway expressed with two different electron donors in Saccharomyces cerevisiae at aerobic growth. , 2015, FEMS yeast research.

[117]  J. Keasling,et al.  Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering. , 2015, Metabolic engineering.